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https://www.readbyqxmd.com/read/28431137/trapp-webserver-predicting-protein-binding-site-flexibility-and-detecting-transient-binding-pockets
#1
Antonia Stank, Daria B Kokh, Max Horn, Elena Sizikova, Rebecca Neil, Joanna Panecka, Stefan Richter, Rebecca C Wade
The TRAnsient Pockets in Proteins (TRAPP) webserver provides an automated workflow that allows users to explore the dynamics of a protein binding site and to detect pockets or sub-pockets that may transiently open due to protein internal motion. These transient or cryptic sub-pockets may be of interest in the design and optimization of small molecular inhibitors for a protein target of interest. The TRAPP workflow consists of the following three modules: (i) TRAPP structure- generation of an ensemble of structures using one or more of four possible molecular simulation methods; (ii) TRAPP analysis-superposition and clustering of the binding site conformations either in an ensemble of structures generated in step (i) or in PDB structures or trajectories uploaded by the user; and (iii) TRAPP pocket-detection, analysis, and visualization of the binding pocket dynamics and characteristics, such as volume, solvent-exposed area or properties of surrounding residues...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28418968/ethereal-notes-from-morrisville-vermont-j-a-robinson-and-maria-von-trapp
#2
(no author information available yet)
No abstract text is available yet for this article.
May 2017: Anesthesiology
https://www.readbyqxmd.com/read/28413256/dynamics-of-postcombustion-co2-capture-plants-modeling-validation-and-case-study
#3
Adam van de Haar, Carsten Trapp, Kai Wellner, Robert de Kler, Gerhard Schmitz, Piero Colonna
The capture of CO2 from power plant flue gases provides an opportunity to mitigate emissions that are harmful to the global climate. While the process of CO2 capture using an aqueous amine solution is well-known from experience in other technical sectors (e.g., acid gas removal in the gas processing industry), its operation combined with a power plant still needs investigation because in this case, the interaction with power plants that are increasingly operated dynamically poses control challenges. This article presents the dynamic modeling of CO2 capture plants followed by a detailed validation using transient measurements recorded from the pilot plant operated at the Maasvlakte power station in the Netherlands...
February 22, 2017: Industrial & Engineering Chemistry Research
https://www.readbyqxmd.com/read/28407841/cardiovascular-comorbidity-in-inflammatory-rheumatological-conditions
#4
Jürgen Braun, Klaus Krüger, Bernhard Manger, Matthias Schneider, Christof Specker, Hans Joachim Trappe
BACKGROUND: Approximately 1.5 million adults in Germany suffer from an inflammatory rheumatological condition. The most common among these are rheumatoid arthritis and spondyloarthritis-above all axial spondyloarthritis, including ankylosing spondylitis (Bekhterev's disease) and psoriatic arthritis. These systemic inflammatory diseases often affect the heart as well. METHODS: This review is based on pertinent articles retrieved by a selective literature search, on current European guidelines, and on the authors' clinical experience...
March 24, 2017: Deutsches Ärzteblatt International
https://www.readbyqxmd.com/read/28406989/escdl-1-a-new-cell-line-derived-from-chicken-embryonic-stem-cells-supports-efficient-replication-of-mardiviruses
#5
Jean-François Vautherot, Christian Jean, Laetitia Fragnet-Trapp, Sylvie Rémy, Danièle Chabanne-Vautherot, Guillaume Montillet, Aurélie Fuet, Caroline Denesvre, Bertrand Pain
Marek's disease virus is the etiological agent of a major lymphoproliferative disorder in poultry and the prototype of the Mardivirus genus. Primary avian somatic cells are currently used for virus replication and vaccine production, but they are largely refractory to any genetic modification compatible with the preservation of intact viral susceptibility. We explored the concept of induction of viral replication permissiveness in an established pluripotent chicken embryonic stem cell-line (cES) in order to derive a new fully susceptible cell-line...
2017: PloS One
https://www.readbyqxmd.com/read/28317203/attracting-enantiomers-chiral-analytes-that-are-simultaneously-shift-reagents-allow-rapid-screening-of-enantiomeric-ratios-by-nmr-spectroscopy
#6
Golo Storch, Maren Haas, Oliver Trapp
The rapid and direct determination of enantiomeric ratios is of increasing interest due to the significantly reduced effort compared to chromatographic methods and the large number of analytes, for instance in enantioselective catalysis. Current strategies include colorimetric assays, (a)chiral solvating reagents for NMR spectroscopy and metal complexes for CD sensing. We report the determination of enantiomeric ratios based on the self-induced diastereomeric anisochronism (SIDA) effect. Alanine derivatives that represent chiral products of enantioselective catalysis, such as the well-established hydrogenation of dehydroamino acids, were investigated...
March 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28295745/does-alcohol-outlet-density-differ-by-area-level-disadvantage-in-metropolitan-perth
#7
Sarah Foster, Paula Hooper, Matthew Knuiman, Georgina Trapp, Lisa Wood
INTRODUCTION AND AIMS: Research suggests that there are area-level disparities in alcohol outlets, with greater density in disadvantaged areas. In part, this might be explained by the inequitable distribution of retail, attracted by lower rents to disadvantaged neighbourhoods. This ecological study examines the distribution of liquor licences in Perth, Australia, and whether discrepancies in the distribution of retail land-uses could account for a socio-economic gradient. DESIGN AND METHODS: Area disadvantage was determined for each Statistical Area 1 (SA1) using the Australian Bureau of Statistics Index of Relative Socio-economic Disadvantage, and licence locations were mapped in GIS...
March 13, 2017: Drug and Alcohol Review
https://www.readbyqxmd.com/read/28295017/antimicrobial-peptide-gramicidin-s-is-accumulated-in-granules-of-producer-cells-for-storage-of-bacterial-phosphagens
#8
Marina Berditsch, Mareike Trapp, Sergii Afonin, Christian Weber, Julia Misiewicz, Joana Turkson, Anne S Ulrich
Many antimicrobial peptides are synthesized non-ribosomally in bacteria, but little is known about their subcellular route of biosynthesis, their mode of intracellular accumulation, or their role in the physiology of the producer cells. Here, we present a comprehensive view on the biosynthesis of gramicidin S (GS) in Aneurinibacillus migulanus, having observed a peripheral membrane localization of its synthetases. The peptide gets accumulated in nano-globules, which mature by fusion into larger granules and end up within vacuolar structures...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28282051/by-design-enantioselective-self-amplification-based-on-non-covalent-product-catalyst-interactions
#9
Golo Storch, Oliver Trapp
The synthesis of enantiomerically pure compounds is of great importance in pharmaceuticals, fragrances and biological applications, and functions as a key to many processes in nature. Asymmetric catalysis using enantiomerically pure catalysts represents an efficient synthetic method to achieve this goal. The enantiomeric excess of the reaction product correlates with the enantiomeric purity of the catalysts, except for nonlinear behaviour, therefore the use of stereochemically flexible catalysts seems to complicate the control of stereoselectivity...
February 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28274122/online-continuous-trace-process-analytics-using-multiplexing-gas-chromatography
#10
Marco R Wunsch, Rudolf Lehnig, Oliver Trapp
The analysis of impurities at a trace level in chemical products, nutrition additives, and drugs is highly important to guarantee safe products suitable for consumption. However, trace analysis in the presence of a dominating component can be a challenging task because of noncompatible linear detection ranges or strong signal overlap that suppresses the signal of interest. Here, we developed a technique for quantitative analysis using multiplexing gas chromatography (mpGC) for continuous and completely automated process trace analytics exemplified for the analysis of a CO2 stream in a production plant for detection of benzene, toluene, ethylbenzene, and the three structural isomers of xylene (BTEX) in the concentration range of 0-10 ppb...
March 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28258014/liquor-landscapes-does-access-to-alcohol-outlets-influence-alcohol-consumption-in-young-adults
#11
Sarah Foster, Georgina Trapp, Paula Hooper, Wendy H Oddy, Lisa Wood, Matthew Knuiman
Few longitudinal studies have examined the impact of liquor licences on alcohol consumption, and none in young adults, the life stage when alcohol intake is at its highest. We examined associations between liquor licences (i.e., general licences, on-premise licences, liquor stores, and club licences) and alcohol consumption at 20-years (n=988) and 22-years (n=893), and whether changes in the licences between time-points influenced alcohol consumption (n=665). Only general licences were associated with alcohol consumption at 20-years (p=0...
February 28, 2017: Health & Place
https://www.readbyqxmd.com/read/28256758/porphyrin-donor-and-tunable-push-pull-acceptor-conjugates-experimental-investigation-of-marcus-theory
#12
Tristan Reekie, Michael Sekita, Lorenz Urner, Stefan Bauroth, Laurent Ruhlamann, Jean-Paul Gisselbrecht, Corinne Boudon, Nils Trapp, Timothy Clark, François Diederich, Dirk Michael Guldi
We report on a series of electron donor-acceptor conjugates incorporating a ZnII porphyrin-based electron donor and a variety of non-conjugated rigid linkers connecting to push-pull chromophores as electron acceptors. The electron acceptors comprize multicyanobutadienes or extended tetracyanoquinodimethane analogues with first reduction potentials ranging from -1.67 to -0.23 V vs. Fc+/Fc in CH2Cl2, which are accessible through a final-step cycloaddition-retroelectrocyclization (CA-RE) reaction. Characterization of the conjugates includes electrochemistry, spectroelectrochemistry, DFT calculations, and photophysical measurements in a range of solvents...
March 3, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28254380/glyceroneogenesis-in-the-hepatopancreas-of-the-crab-neohelice-granulata-diet-starvation-and-season-effects
#13
E Sarapio, J T Santos, J F A Model, L S De Fraga, A S Vinagre, T L Martins, R S M Da Silva, M Trapp
We determined the activity of glyceroneogenesis from [2-(14)C]-pyruvate, the phosphoenolpyruvate carboxykinase activity, [2-(14)C]-pyruvate oxidation and total lipid levels in the hepatopancreas of the crab Neohelice granulata fed with a carbohydrate-rich (HC) diet or a high-protein (HP) diet and then subjected to 5weeks of starvation, in summer and winter, to determine whether the seasonal adjustments of lipid metabolism to food scarcity are modulated by the composition of the diet previously given to the crabs...
February 22, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28240221/mammalian-trappiii-complex-positively-modulates-the-recruitment-of-sec13-31-onto-copii-vesicles
#14
Shan Zhao, Chun Man Li, Xiao Min Luo, Gavin Ka Yu Siu, Wen Jia Gan, Lin Zhang, William K K Wu, Hsiao Chang Chan, Sidney Yu
The Transport protein particle (TRAPP) complex is a tethering factor for COPII vesicle. Of three forms of TRAPP (TRAPPI, II and III) complexes identified so far, TRAPPIII has been largely considered to play a role in autophagy. While depletion of TRAPPIII specific subunits caused defects in the early secretory pathway and TRAPPIII might interact with components of the COPII vesicle coat, its exact role remains to be determined. In this study, we studied the function of TRAPPIII in early secretory pathway using a TRAPPIII-specific subunit, TRAPPC12, as starting point...
February 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28215353/a-molecular-and-morphological-re-examination-of-the-generic-limits-of-truffles-in-the-tarzetta-geopyxis-lineage-densocarpa-hydnocystis-and-paurocotylis
#15
Leticia M Kumar, Matthew E Smith, Eduardo R Nouhra, Takamichi Orihara, Pablo Sandoval Leiva, Donald H Pfister, David J McLaughlin, James M Trappe, Rosanne A Healy
Truffle species within the /tarzetta-geopyxis lineage share smooth, globose, hyaline spores, but differ in the amount of convolution of hymenia in ascomata. The relationships among truffle species in this lineage have historically been confused. Phylogenetic analyses of the ITS and 28S nuclear ribosomal DNA from recently collected members of the /tarzetta-geopyxis lineage from Asia, Austral Asia, North America, and South America prompted a reinvestigation of species and generic limits in the truffle genera Hydnocystis, Paurocotylis, and Stephensia...
March 2017: Fungal Biology
https://www.readbyqxmd.com/read/28204917/-ecg-score-to-predict-icd-therapies-in-patients-with-nonischemic-cardiomyopathy-and-primary-prophylactic-crt-d
#16
Martin Grett, Martin Christ, Jan-Peter Röing Gen Nölke, Hans-Joachim Trappe
BACKGROUND AND PROBLEM: Recently published results of the DANISH study raise concerns, if primary prophylactic ICD implantations in patients with nonischemic cardiomyopathy (NICM) and severe reduced left ventricular ejection fraction (LVEF) should be performed without further risk stratification. There was no significant difference in the overall mortality of patients with or without ICD and CRT defibrillator (CRT-D) or CRT pacemaker (CRT-P), respectively. Clinical risk scores to identify patients with ischemic cardiomyopathy (ICM) who benefit most from an ICD have been recommended...
February 15, 2017: Herzschrittmachertherapie & Elektrophysiologie
https://www.readbyqxmd.com/read/28199103/using-the-k-d-tree-data-structure-to-accelerate-monte-carlo-simulations
#17
Qile P Chen, Bai Xue, J Ilja Siepmann
The k-d tree data structure is implemented in a Monte Carlo (MC) molecular simulation program to accelerate the range search for particles or interaction sites within the cutoff distance when Lennard-Jones and Coulomb interactions are computed. MC simulations are performed for different molecules in various ensembles to assess the efficiency enhancements due to the k-d tree data structure. It is found that the use of k-d trees accelerates significantly simulations for Lennard-Jones particles in the NVT and NVT-Gibbs ensembles and for n-butane and 2,4,6,8,10,12,14,16,18,20,22-undecamethylpentacosane represented by the TraPPE-UA force field in the NpT ensemble...
March 6, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28191691/bace1-regulates-the-proliferation-and-cellular-functions-of-schwann-cells
#18
Xiangyou Hu, Hailong Hou, Chinthasagar Bastian, Wanxia He, Shupeng Qiu, Yingying Ge, Xinhua Yin, Grahame J Kidd, Sylvain Brunet, Bruce D Trapp, Selva Baltan, Riqiang Yan
BACE1 is an indispensable enzyme for generating β-amyloid peptides, which are excessively accumulated in brains of Alzheimer's patients. However, BACE1 is also required for proper myelination of peripheral nerves, as BACE1-null mice display hypomyelination. To determine the precise effects of BACE1 on myelination, here we have uncovered a role of BACE1 in the control of Schwann cell proliferation during development. We demonstrate that BACE1 regulates the cleavage of Jagged-1 and Delta-1, two membrane-bound ligands of Notch...
May 2017: Glia
https://www.readbyqxmd.com/read/28190761/prevalence-of-circulating-tumor-cells-after-adjuvant-chemotherapy-with-or-without-anthracyclines-in-patients-with-her2-negative-hormone-receptor-positive-early-breast-cancer
#19
Amelie Schramm, Fabienne Schochter, Thomas W P Friedl, Nikolaus de Gregorio, Ulrich Andergassen, Marianna Alunni-Fabbroni, Elisabeth Trapp, Bernadette Jaeger, Georg Heinrich, Oumar Camara, Thomas Decker, Angelika Ober, Sven Mahner, Tanja N Fehm, Klaus Pantel, Peter A Fasching, Andreas Schneeweiss, Wolfgang Janni, Brigitte K Rack
BACKGROUND: Use of anthracycline-based chemotherapy in patients with early breast cancer (EBC) has been well-established but is often associated with cardiotoxicity. Based on data suggesting a limited benefit of anthracyclines in human epidermal growth factor receptor 2 (HER2)-negative patients, the Simultaneous Study of Docetaxel Based Anthracycline Free Adjuvant Treatment Evaluation, as well as Life Style Intervention Strategies (SUCCESS) C study randomized patients to either anthracycline-containing or anthracycline-free chemotherapy...
January 10, 2017: Clinical Breast Cancer
https://www.readbyqxmd.com/read/28190358/submerged-cultivation-of-pleurotus-sapidus-with-molasses-aroma-dilution-analyses-by-means-of-solid-phase-microextraction-and-stir-bar-sorptive-extraction
#20
Tobias Trapp, Martina Zajul, Jenny Ahlborn, Alexander Stephan, Holger Zorn, Marco Alexander Fraatz
The basidiomycete Pleurotus sapidus (PSA) was grown in submerged cultures with molasses as substrate for the production of mycelium as a protein source for food applications. The volatilomes of the substrate, the submerged culture, and the mycelia were analyzed by gas chromatography-tandem mass spectrometry-olfactometry. For compound identification, aroma dilution analyses by means of headspace solid phase microextraction and stir bar sorptive extraction were performed via variation of the split vent flow rate...
February 11, 2017: Journal of Agricultural and Food Chemistry
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